メチル共酵素M還元酵素のメカニズムにはNi-メチル中間体があるのでしょうか?
Shi-lu Chen1, Vladimir Pelmenschikov, Margareta R A Blomberg
1Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden. shlchen@physto.se
Journal of the American Chemical Society
|July 3, 2009
まとめ
メチル-コエンザイムM還元酵素 (MCR) のメチル-ニール (Methyl-Ni(F(430)) の形成は,基質の酸性に依存する. メチルハリドはこれを促進するが,原生基板はエネルギー的にアクセス不能であり,実験結果と一致する.
科学分野:
- バイオケミストリー バイオケミストリー
- コンピューティング・ケミストリー
- 酵素学 酵素学とは
背景:
- メチル共酵素M還元酵素 (MCR) は,メタノゲネシスに不可欠です.
- 活性部位,特にメチル-Ni(F(430)) の形成を理解することは,MCRの機能の鍵です.
- 以前の研究では,様々な基板でMCRメカニズムを調査しました.
研究 の 目的:
- MCR.におけるメチル-Ni(F(430)) 種の形成経路を調査する.
- メチル-Ni(F(430)) の形成に基質を離れるグループの酸性の影響を決定する.
- メチル-ニオール (((F ((430)) 形成のエネルギー可行性を,原生基板を含む異なる基板と比較する.
主な方法:
- 理論的な計算のためにB3LYPハイブリッド密度関数法を使用しました.
- MCRのX線結晶構造から派生したアクティブサイトモデルを使用した.
- メチルヨウ酸化物,メチルブロミド,メチル塩化物,およびジメチル硫化物を基質として使用したシミュレーション反応.
主要な成果:
- 計算により,メチル-Ni(F(430)) の形成は,基質の離脱グループの酸性によって有意に影響されていることが明らかになった.
- メチル-Ni(F(430)) 種は,メチルハリド基板で計算的に観察されました.
- エネルギー分析は,ネイティブ基板 (メチル共酵素M) からメチル-Ni(F(430)) を形成することがエネルギー的に不利であることを示しました.
結論:
- 脱出グループの酸性は,MCRにおけるメチル-Ni(F(430)) の形成を制御する重要な要因である.
- メチルハリドは,ネイティブ基板よりもメチル-Ni (((F (((430)) 種を形成するのに有利です.
- 計算上の発見は,MCR活動に関する既存の実験的観測と一致しています.
関連する概念動画
Phase II Reactions: Methylation Reactions
Methylation is a phase II biotransformation process involving the attachment of a methyl group to a substrate. Enzymes known as methyltransferases orchestrate this reaction.
The mechanism of methylation unfolds in two stages. The first stage sees a methyltransferase enzyme facilitating the transfer of a methyl group from S-adenosylmethionine (SAM) to the substrate, forming S-adenosylhomocysteine (SAH). The second stage involves further metabolism of SAH into homocysteine, which can be recycled...
The mechanism of methylation unfolds in two stages. The first stage sees a methyltransferase enzyme facilitating the transfer of a methyl group from S-adenosylmethionine (SAM) to the substrate, forming S-adenosylhomocysteine (SAH). The second stage involves further metabolism of SAH into homocysteine, which can be recycled...
Rate-Determining Steps
Relating Reaction Mechanisms
In a multistep reaction mechanism, one of the elementary steps progresses significantly slower than the others. This slowest step is called the rate-limiting step (or rate-determining step). A reaction cannot proceed faster than its slowest step, and hence, the rate-determining step limits the overall reaction rate.
The concept of rate-determining step can be understood from the analogy of a 4-lane freeway with a short-stretch of traffic-bottleneck caused due to...
In a multistep reaction mechanism, one of the elementary steps progresses significantly slower than the others. This slowest step is called the rate-limiting step (or rate-determining step). A reaction cannot proceed faster than its slowest step, and hence, the rate-determining step limits the overall reaction rate.
The concept of rate-determining step can be understood from the analogy of a 4-lane freeway with a short-stretch of traffic-bottleneck caused due to...
Electron Transport Chain: Complex I and II
The mitochondrial electron transport chain (ETC) is the main energy generation system in the eukaryotic cells. However, mitochondria also produce cytotoxic reactive oxygen species (ROS) due to the large electron flow during oxidative phosphorylation. While Complex I is one of the primary sources of superoxide radicals, ROS production by Complex II is uncommon and may only be observed in cancer cells with mutated complexes.
ROS generation is regulated and maintained at moderate levels necessary...
ROS generation is regulated and maintained at moderate levels necessary...
Preparation of Amines: Reductive Amination of Aldehydes and Ketones
Carbonyl compounds and primary amines undergo reductive amination first to produce imines, followed by secondary amines in the same reaction mixture, using selective reducing agents like sodium cyanoborohydride or sodium triacetoxyborohydride. Reductive amination produces different degrees of substitution of amines depending on the starting amine substrate.
Role of Reduced Coenzymes NADH and FADH₂
The energy released from the breakdown of the chemical bonds within nutrients can be stored either through the reduction of electron carriers or in the bonds of adenosine triphosphate (ATP). In living systems, a small class of compounds functions as mobile electron carriers, molecules that bind to and shuttle high-energy electrons between compounds in pathways. The principal electron carriers that will be considered originate from the B vitamin group and are derivatives of nucleotides; they are...
Preparation of Amines: Reduction of Amides and Nitriles
Nitriles can be reduced to primary amines using reducing agents like lithium aluminum hydride or catalytic hydrogenation. The reduction introduces an amino group with an extra carbon in the skeleton. Nitriles are formed from the reaction between alkyl halides and sodium cyanide through the SN2 mechanism. Primary alkyl halides are the preferred substrates to prepare nitriles.
Amides can be reduced to primary, secondary, and tertiary amines using catalytic hydrogenation, active metals like Fe,...
Amides can be reduced to primary, secondary, and tertiary amines using catalytic hydrogenation, active metals like Fe,...


